If I could make a suggestion, from what I read in this thread (haven't played the hack yet, I only play completed hacks), it is more than possible in a few situations for the player to defeat a trainer when they should, according to the story, lose, causing the game to act as if the player lost the battle when they really won it.

To me, that is bad game design and really awkward in general. I would suggest putting Pokemon on the teams of trainers you are supposed to lose to at level 100, with their stats all at 999, so that way, it is obvious to the player that they are to lose that particular battle, and it makes more sense storyline wise, rather than creating this awkward situation of having a trainer get beaten into the ground, but then having said trainer gloat about their "victory".

Also, please consider making sequel hacks for the Johto and Hoenn regions as well (although if you could fit Johto in this hack, that would be great!). Of course, if you wanted to go even further and do the regions after Hoenn, that would be perfectly fine with me .